I found out that the legends and tooltips break in RTL. The legends labels overlap the colored boxes and the text within the labels is pushed outside of the tooltip box.
I managed to make the tooltips presentable through the use of
$chart['#tooltips_use_html'] = TRUE; (in 'chart_alter'). Although the text is aligned wrongly the out of box issue disappeared.
However I found no similar option for the legend. I looked at the Highcharts documentation where I found a
useHTML option for fixing this issue with legends. But I am unsure about how to apply it with the hooks provided by the Charts module.
Here is a picture of it: